Transcriptome analysis reveals positive selection on the divergent between topmouth culter and zebrafish

• 27,741 unigenes from the topmouth culter liver produce 11,131 annotated genes.
• 4 genes of the zebrafish orthologs exhibit strong positive selection.
• 3111 simple repeat sequences of different patterns were also obtained.
• 38 candidate positive selection genes were extracted from 4033 orthologs.
• The topmouth culter–zebrafish separation was dated to 64 MYA.

The topmouth culter (Erythroculter ilishaeformis) is a predatory cyprinid fish that distributes widely in the East Asia. Here we report the liver transcriptome in this organism as a model of predatory fish. Sequencing of 5 Gb raw reads led to 27,741 unigenes and produced 11,131 annotatable genes. A total of 7093 (63.7%) genes were found to have putative functions by gene ontology analysis. Importantly, a blast search revealed 4033 culter genes that were orthologous to the zebrafish. Extracted from 38 candidate positive selection genes, 4 genes exhibit strong positive selection based on the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks). In addition, the four genes also indicated the strong positive selection by comparing them between blunt snout bream (Megalobrama amblycephala) and zebrafish. These genes were involved in activator of gene expression, metabolic processes and development. The transcriptome variation may be reflective of natural selection in the early life history of Cyprinidae. Based on Ks ratios, date of the separation between topmouth culter and zebrafish is approximately 64 million years ago. We conclude that natural selection acts in diversifying the genomes between topmouth culter and zebrafish.